NP-MRD: Showing NP-Card for Deacetylnomilin (NP0048289)

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Record Information

Version

2.0

Created at

2022-03-17 20:54:05 UTC

Updated at

2022-03-17 20:54:05 UTC

NP-MRD ID

NP0048289

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Deacetylnomilin

Description

Deacetylnomilin, also known as isolimonin, belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17. Deacetylnomilin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, deacetylnomilin has been detected, but not quantified in, several different foods, such as citrus, lemons, mandarin orange (clementine, tangerine), and sweet oranges. Deacetylnomilin is found in Citrus hanaju, Citrus ichangensis and Microcitrus australasica . This could make deacetylnomilin a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061308382D          

 34 39  0  0  0  0            999 V2000
    4.2725    2.0506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2964    1.9508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0012   -0.9874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3681   -0.4691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1035    0.1209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6176   -0.6563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6729   -1.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8094   -0.8219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1830   -2.4878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3999    1.6918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9571   -0.4801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5936   -1.4020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1929   -1.1529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8784    0.1264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9474    1.0746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1360   -0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5917    1.5263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5316    0.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4537   -0.3702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9752    1.1952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1670    1.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7219    1.3587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2619   -0.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6866    0.2919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3309    0.7435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5227    0.5780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7076   -1.1050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1326    1.9077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3143   -0.1488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3804    1.6469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5997   -2.2270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0938    0.2470    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4270    0.9303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7835    1.3607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 13  7  1  0  0  0  0
 13 12  2  0  0  0  0
 14  6  1  0  0  0  0
 15 10  1  0  0  0  0
 16 11  1  0  0  0  0
 17 10  1  0  0  0  0
 18 11  1  0  0  0  0
 19 13  1  0  0  0  0
 21 20  1  0  0  0  0
 22  1  1  0  0  0  0
 22  2  1  0  0  0  0
 22 15  1  0  0  0  0
 23  3  1  0  0  0  0
 23  8  1  0  0  0  0
 23 19  1  0  0  0  0
 24  4  1  0  0  0  0
 24 14  1  0  0  0  0
 24 15  1  0  0  0  0
 24 16  1  0  0  0  0
 25  5  1  0  0  0  0
 25 14  1  0  0  0  0
 25 17  1  0  0  0  0
 26 20  1  0  0  0  0
 26 23  1  0  0  0  0
 26 25  1  0  0  0  0
 27 16  1  0  0  0  0
 28 17  2  0  0  0  0
 29 18  2  0  0  0  0
 30 21  2  0  0  0  0
 31  9  1  0  0  0  0
 31 12  1  0  0  0  0
 32 19  1  0  0  0  0
 32 21  1  0  0  0  0
 33 18  1  0  0  0  0
 33 22  1  0  0  0  0
 34 20  1  0  0  0  0
 34 26  1  0  0  0  0
M  END


  Mrv0541 05061308382D          

 34 39  0  0  0  0            999 V2000
    4.2725    2.0506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2964    1.9508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0012   -0.9874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3681   -0.4691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1035    0.1209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6176   -0.6563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6729   -1.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8094   -0.8219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1830   -2.4878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3999    1.6918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9571   -0.4801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5936   -1.4020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1929   -1.1529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8784    0.1264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9474    1.0746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1360   -0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5917    1.5263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5316    0.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4537   -0.3702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9752    1.1952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1670    1.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7219    1.3587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2619   -0.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6866    0.2919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3309    0.7435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5227    0.5780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7076   -1.1050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1326    1.9077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3143   -0.1488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3804    1.6469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5997   -2.2270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0938    0.2470    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4270    0.9303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7835    1.3607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 13  7  1  0  0  0  0
 13 12  2  0  0  0  0
 14  6  1  0  0  0  0
 15 10  1  0  0  0  0
 16 11  1  0  0  0  0
 17 10  1  0  0  0  0
 18 11  1  0  0  0  0
 19 13  1  0  0  0  0
 21 20  1  0  0  0  0
 22  1  1  0  0  0  0
 22  2  1  0  0  0  0
 22 15  1  0  0  0  0
 23  3  1  0  0  0  0
 23  8  1  0  0  0  0
 23 19  1  0  0  0  0
 24  4  1  0  0  0  0
 24 14  1  0  0  0  0
 24 15  1  0  0  0  0
 24 16  1  0  0  0  0
 25  5  1  0  0  0  0
 25 14  1  0  0  0  0
 25 17  1  0  0  0  0
 26 20  1  0  0  0  0
 26 23  1  0  0  0  0
 26 25  1  0  0  0  0
 27 16  1  0  0  0  0
 28 17  2  0  0  0  0
 29 18  2  0  0  0  0
 30 21  2  0  0  0  0
 31  9  1  0  0  0  0
 31 12  1  0  0  0  0
 32 19  1  0  0  0  0
 32 21  1  0  0  0  0
 33 18  1  0  0  0  0
 33 22  1  0  0  0  0
 34 20  1  0  0  0  0
 34 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048289

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC12CCC3C4(C)C(CC(=O)C3(C)C11OC1C(=O)OC2C1=COC=C1)C(C)(C)OC(=O)CC4O

> <INCHI_IDENTIFIER>
InChI=1S/C26H32O8/c1-22(2)15-10-17(28)25(5)14(24(15,4)16(27)11-18(29)33-22)6-8-23(3)19(13-7-9-31-12-13)32-21(30)20-26(23,25)34-20/h7,9,12,14-16,19-20,27H,6,8,10-11H2,1-5H3

> <INCHI_KEY>
HWAJASVMTDEFJN-UHFFFAOYSA-N

> <FORMULA>
C26H32O8

> <MOLECULAR_WEIGHT>
472.5275

> <EXACT_MASS>
472.209718

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
48.37774004160755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-(furan-3-yl)-13-hydroxy-1,8,12,17,17-pentamethyl-3,6,16-trioxapentacyclo[9.9.0.0²,⁴.0²,⁸.0¹²,¹⁸]icosane-5,15,20-trione

> <ALOGPS_LOGP>
2.70

> <JCHEM_LOGP>
2.576258725333332

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.50166460077634

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.417265493119736

> <JCHEM_PKA_STRONGEST_BASIC>
-3.053322192083649

> <JCHEM_POLAR_SURFACE_AREA>
115.57000000000001

> <JCHEM_REFRACTIVITY>
116.45459999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.41e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-(furan-3-yl)-13-hydroxy-1,8,12,17,17-pentamethyl-3,6,16-trioxapentacyclo[9.9.0.0²,⁴.0²,⁸.0¹²,¹⁸]icosane-5,15,20-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       7.975   3.828   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.887   3.641   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.869  -1.843   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.287  -0.876   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.927   0.226   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.886  -1.225   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.256  -3.405   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.378  -1.534   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.342  -4.644   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.346   3.158   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.253  -0.896   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.108  -2.617   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.360  -2.152   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.373   0.236   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.368   2.006   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.721  -0.747   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.838   2.849   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.326   0.209   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.847  -0.691   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.820   2.231   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.312   1.922   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.814   2.536   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.356  -0.382   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.882   0.545   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.351   1.388   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.842   1.079   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.921  -2.063   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.981   3.561   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      11.787  -0.278   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -0.710   3.074   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.119  -4.157   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -0.175   0.461   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      10.130   1.737   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       3.329   2.540   0.000  0.00  0.00           O+0
CONECT    1   22                                                            
CONECT    2   22                                                            
CONECT    3   23                                                            
CONECT    4   24                                                            
CONECT    5   25                                                            
CONECT    6    8   14                                                       
CONECT    7    9   13                                                       
CONECT    8    6   23                                                       
CONECT    9    7   31                                                       
CONECT   10   15   17                                                       
CONECT   11   16   18                                                       
CONECT   12   13   31                                                       
CONECT   13    7   12   19                                                  
CONECT   14    6   24   25                                                  
CONECT   15   10   22   24                                                  
CONECT   16   11   24   27                                                  
CONECT   17   10   25   28                                                  
CONECT   18   11   29   33                                                  
CONECT   19   13   23   32                                                  
CONECT   20   21   26   34                                                  
CONECT   21   20   30   32                                                  
CONECT   22    1    2   15   33                                             
CONECT   23    3    8   19   26                                             
CONECT   24    4   14   15   16                                             
CONECT   25    5   14   17   26                                             
CONECT   26   20   23   25   34                                             
CONECT   27   16                                                            
CONECT   28   17                                                            
CONECT   29   18                                                            
CONECT   30   21                                                            
CONECT   31    9   12                                                       
CONECT   32   19   21                                                       
CONECT   33   18   22                                                       
CONECT   34   20   26                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Value	Source
Isolimonin	HMDB

Chemical Formula

C₂₆H₃₂O₈

Average Mass

472.5275 Da

Monoisotopic Mass

472.20972 Da

IUPAC Name

7-(furan-3-yl)-13-hydroxy-1,8,12,17,17-pentamethyl-3,6,16-trioxapentacyclo[9.9.0.0²,⁴.0²,⁸.0¹²,¹⁸]icosane-5,15,20-trione

Traditional Name

7-(furan-3-yl)-13-hydroxy-1,8,12,17,17-pentamethyl-3,6,16-trioxapentacyclo[9.9.0.0²,⁴.0²,⁸.0¹²,¹⁸]icosane-5,15,20-trione

CAS Registry Number

3264-90-2

SMILES

CC12CCC3C4(C)C(CC(=O)C3(C)C11OC1C(=O)OC2C1=COC=C1)C(C)(C)OC(=O)CC4O

InChI Identifier

InChI=1S/C26H32O8/c1-22(2)15-10-17(28)25(5)14(24(15,4)16(27)11-18(29)33-22)6-8-23(3)19(13-7-9-31-12-13)32-21(30)20-26(23,25)34-20/h7,9,12,14-16,19-20,27H,6,8,10-11H2,1-5H3

InChI Key

HWAJASVMTDEFJN-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Citrus hanaju	LOTUS Database	35616633
Citrus ichangensis	Plant	KNApSAcK
Citrus limon	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Citrus reticulata	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Citrus X sinensis (L.) Osbeck (pro. sp.)	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Microcitrus australasica	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Limonoids

Alternative Parents

Substituents

Limonoid skeleton
Naphthopyran
Naphthalene
Caprolactone
1,4-dioxepane
Delta valerolactone
Dioxepane
Delta_valerolactone
Oxepane
Oxane
Pyran
Dicarboxylic acid or derivatives
Heteroaromatic compound
Furan
Secondary alcohol
Carboxylic acid ester
Lactone
Ketone
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Dialkyl ether
Oxirane
Ether
Organic oxide
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	2.7	ALOGPS
logP	2.58	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	14.42	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	115.57 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	116.45 m³·mol⁻¹	ChemAxon
Polarizability	48.38 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0035684

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014401

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13857953

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Deacetylnomilin (NP0048289)

MOL for NP0048289 (Deacetylnomilin)

3D MOL for NP0048289 (Deacetylnomilin)

3D SDF for NP0048289 (Deacetylnomilin)

3D-SDF for NP0048289 (Deacetylnomilin)

PDB for NP0048289 (Deacetylnomilin)

3D PDB for NP0048289 (Deacetylnomilin)

SMILES for NP0048289 (Deacetylnomilin)

INCHI for NP0048289 (Deacetylnomilin)

Structure for NP0048289 (Deacetylnomilin)

3D Structure for NP0048289 (Deacetylnomilin)